From an objective critical viewpoint:
1. Mario Galaxy 2
2. Resident Evil 4
3. Mario Galaxy
4. Mario Bros. 3
5. Bioshock
6. Zelda: Ocarina of Time
7. Half Life 2
8. Banjo Kazooie
9. Donkey Kong Country 2
10. Soul Calibur
My personal favourites:
1. Resident Evil 4
2. Mario Galaxy 2
3. Mario Galaxy
4. Starfox (SNES)
5. Starfox 2 (SNES)
6. Dead Space
7. NiGHTS into Dreams
8. Gears of War 2
9. Sin and Punishment 2
10. F Zero GX